file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
length(assayed_genes)## [1] 2000
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 35.0 38.0 39.0 39.1 41.0 42.0
## [1] 40
## [1] 35 35 37 37 37 37 37 37 38 38 38 38 38 38 39 39 39 39 39 39 39 39 39 39 39
## [26] 39 40 41 41 41 41 41 41 41 41 41 41 42 42 42
alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}
table(is.na(a2s))##
## FALSE TRUE
## 1739 261
##
## FALSE TRUE <NA>
## 21 1718 261
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: LRRC6 DNAAF11
## 2: C11orf49 CSTPP1
## 3: LINC00476 ERCC6L2-AS1
## 4: HNRNPA1P48 HNRNPA1L3
## 5: ZRANB2-AS2 ZRANB2-DT
## 6: LINC00271 AHI1-DT
## 7: RFX3-AS1 RFX3-DT
## 8: LINC00884 ATP13A3-DT
## 9: FBXO30-DT EPM2A-DT
## 10: LINC00894 EOLA2-DT
## 11: COX10-AS1 COX10-DT
## 12: LINC01184 SLC12A2-DT
## 13: FAM198B-AS1 GASK1B-AS1
## 14: C5orf17 LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16: LINC01146 HISLA
## 17: BTBD11 ABTB3
## 18: H2BU1 H2BC26
## 19: SKIV2L SKIC2
## 20: FAM155A NALF1
## 21: CTB-41I6.2 PIK3R5-DT
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1
## 3: PDK4 PDK4 PDK4
## 4: CALCR CALCR CALCR
## 5: ABCB4 ABCB4 ABCB4
## t1
## 1
## 2000
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
## [1] 1587110 4
## Gene Gene name Cell type nTPM
## 1: ENSG00000000003 TSPAN6 Adipocytes 149.5
## 2: ENSG00000000003 TSPAN6 Alveolar cells type 1 6.1
## 3: ENSG00000000003 TSPAN6 Alveolar cells type 2 10.5
## 4: ENSG00000000003 TSPAN6 Astrocytes 13.9
## 5: ENSG00000000003 TSPAN6 B-cells 1.5
## [1] 79
##
## Adipocytes Alveolar cells type 1
## 20090 20090
## Alveolar cells type 2 Astrocytes
## 20090 20090
## B-cells Basal keratinocytes
## 20090 20090
## Basal prostatic cells Basal respiratory cells
## 20090 20090
## Basal squamous epithelial cells Bipolar cells
## 20090 20090
## Breast glandular cells Breast myoepithelial cells
## 20090 20090
## Cardiomyocytes Cholangiocytes
## 20090 20090
## Club cells Collecting duct cells
## 20090 20090
## Cone photoreceptor cells Cytotrophoblasts
## 20090 20090
## dendritic cells Distal enterocytes
## 20090 20090
## Distal tubular cells Ductal cells
## 20090 20090
## Early spermatids Endometrial ciliated cells
## 20090 20090
## Endometrial stromal cells Endothelial cells
## 20090 20090
## Enteroendocrine cells Erythroid cells
## 20090 20090
## Excitatory neurons Exocrine glandular cells
## 20090 20090
## Extravillous trophoblasts Fibroblasts
## 20090 20090
## Gastric mucus-secreting cells Glandular and luminal cells
## 20090 20090
## granulocytes Granulosa cells
## 20090 20090
## Hepatocytes Hofbauer cells
## 20090 20090
## Horizontal cells Inhibitory neurons
## 20090 20090
## Intestinal goblet cells Ionocytes
## 20090 20090
## Kupffer cells Langerhans cells
## 20090 20090
## Late spermatids Leydig cells
## 20090 20090
## Macrophages Melanocytes
## 20090 20090
## Microglial cells monocytes
## 20090 20090
## Mucus glandular cells Muller glia cells
## 20090 20090
## NK-cells Oligodendrocyte precursor cells
## 20090 20090
## Oligodendrocytes Pancreatic endocrine cells
## 20090 20090
## Paneth cells Peritubular cells
## 20090 20090
## Plasma cells Prostatic glandular cells
## 20090 20090
## Proximal enterocytes Proximal tubular cells
## 20090 20090
## Respiratory ciliated cells Rod photoreceptor cells
## 20090 20090
## Salivary duct cells Schwann cells
## 20090 20090
## Serous glandular cells Sertoli cells
## 20090 20090
## Skeletal myocytes Smooth muscle cells
## 20090 20090
## Spermatocytes Spermatogonia
## 20090 20090
## Squamous epithelial cells Suprabasal keratinocytes
## 20090 20090
## Syncytiotrophoblasts T-cells
## 20090 20090
## Theca cells Thymic epithelial cells
## 20090 20090
## Undifferentiated cells
## 20090
## [1] 16 2
## Cell_type Cell_group
## 1: Excitatory neurons Neuronal
## 2: Inhibitory neurons Neuronal
##
## Astrocytes B-cells
## 20090 20090
## Bipolar cells Cone photoreceptor cells
## 20090 20090
## Excitatory neurons Horizontal cells
## 20090 20090
## Inhibitory neurons Microglial cells
## 20090 20090
## Muller glia cells Oligodendrocyte precursor cells
## 20090 20090
## Oligodendrocytes Plasma cells
## 20090 20090
## Rod photoreceptor cells Schwann cells
## 20090 20090
## T-cells
## 20090
## [1] 2000 3
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]
n_genes = sum(genes %in% ct$`Gene name`)
print(sprintf("found %d genes.", n_genes))
if(n_genes == 0) { next }
df = ct[`Gene name` %in% genes,]
dim(df)
df[1:2,]
stopifnot(all(str_to_lower(df$`Cell type`) %in%
str_to_lower(cell_group$Cell_type)))
mat1 = match(str_to_lower(df$`Cell type`),
str_to_lower(cell_group$Cell_type))
df = cbind(df, cell_group[mat1,])
df[1:2,]
df$Cell_type = factor(df$Cell_type, levels = cell_group$Cell_type)
df$Cell_group = factor(df$Cell_group,
levels = unique(cell_group$Cell_group))
p1 = ggplot(df, aes(x=Cell_type, y=log10(nTPM + 0.1), fill=Cell_group)) +
geom_boxplot() + xlab("Cell type") + ggtitle(set_k) +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
scale_fill_brewer(palette="RdBu")
print(p1)
}## [1] 1
## [1] "CEACAM1" "HAMP" "DUOX1" "RAB40B"
## [5] "FOLR2" "ADGRG2" "FLJ40194" "DLEU7"
## [9] "FAM177B" "HNRNPA1P48" "EDNRB-AS1" "LINC01375"
## [13] "ENTPD1-AS1" "SLC8A1-AS1" "RP11-142M10.2" "SRGAP2-AS1"
## [17] "AC092431.3" "RNASEH2B-AS1" "RP11-353M9.1" "RP11-666F17.1"
## [21] "RP11-796E2.4" "FAM198B-AS1" "RP11-360F5.1" "AC006160.5"
## [25] "RP11-281P23.2" "RP11-238K6.1" "RP11-649G15.2" "RP11-452H21.1"
## [29] "RP11-513G19.1" "RP11-486A14.2" "RP11-136F16.1" "RP11-370I10.2"
## [33] "RP11-517O13.1" "ABHD15-AS1" "RP11-264E23.4" "RP11-7F3.1"
## [37] "AC009166.9" "RP11-56I23.2" "EME2"
## [1] "found 9 genes."
## [1] 2
## [1] "OSBPL6" "P3H2" "GCNT2" "TENT5A" "RALGPS2" "NRN1"
## [7] "MIS18BP1" "KCNMB1" "AIG1" "SLC25A25" "MAGI1" "PTPN14"
## [13] "KCNMA1" "TIAM1" "TMEM169" "PLEKHA7" "NXN" "S100Z"
## [19] "MBOAT1" "SH3RF3" "NCKAP5" "APOO" "PLEKHA5" "RASSF2"
## [25] "MICU1" "DENND1A" "SLC35E1" "ZBTB46" "STARD13" "DENND4C"
## [31] "SLC12A6" "SRSF12" "AGAP1" "SLC43A2" "FAM110B" "TANC2"
## [37] "SIPA1L1"
## [1] "found 37 genes."
## [1] 3
## [1] "ABCB4" "ARL5C" "AZIN2" "RASGEF1C"
## [5] "TMEM163" "GHRL" "GASK1B" "ADAMTS15"
## [9] "MICOS10" "MARCHF3" "PLCXD3" "KBTBD12"
## [13] "AC007879.5" "RP1-30E17.2" "CCDC26" "AC002539.1"
## [17] "LINC02642" "COX10-AS1" "LINC01141" "KCNMB2-AS1"
## [21] "LINC02008" "RP11-246A10.1" "XACT" "LINC02057"
## [25] "LINC01091" "AC008697.1" "LINC01094" "RP11-745L13.2"
## [29] "CTC-575N7.1" "MAILR" "SMIM35" "RP11-554D14.6"
## [33] "LINC02444" "RP11-588H23.3" "RP11-72M17.1" "RP11-399K21.11"
## [37] "LINC02712" "LINC01374" "RP11-692P14.1" "RP11-321P16.3"
## [41] "RP1-236J16.3"
## [1] "found 13 genes."
## [1] 4
## [1] "BEX1" "ENPP3" "SLC9B1" "GPR85" "TCERG1L"
## [6] "WEE2-AS1" "AC011288.2" "COA6-AS1" "LINC00996" "ZNF528-AS1"
## [11] "TENM1" "FGF14" "ATP8A2" "STXBP5L" "TENM2"
## [16] "CNTN5" "ADGRL3" "ZNF385D" "SPOCK1" "AK5"
## [21] "NCAM2" "CAMK2N1" "GABRB1" "CSMD3" "LRFN5"
## [26] "NEGR1" "FUT9" "KCTD16" "FLRT2" "LSAMP"
## [31] "PTPRT" "TAFA2" "LINC00632" "FAM155A" "MEG3"
## [36] "RP11-191L9.4" "AC093843.1" "SHISA9" "RP11-384F7.2" "AGBL1"
## [41] "IQCJ-SCHIP1"
## [1] "found 30 genes."
## [1] 5
## [1] "RBL1" "PRTFDC1" "DAAM1" "ARHGEF18" "ARSB"
## [6] "LRRC6" "ZSCAN5A" "MTHFS" "RALGPS1" "MAMDC2"
## [11] "ARHGAP42" "CDYL2" "LCLAT1" "SCAI" "LINC00476"
## [16] "C5orf64" "FIGN" "KIAA0825" "CENPP" "SCOC-AS1"
## [21] "RANBP17" "ATP6AP1L" "LIN52" "SLC16A1-AS1" "RP11-120D5.1"
## [26] "RORA-AS1" "LINC00506" "SNX25" "E2F3" "GABRG2"
## [31] "HELLS" "NR6A1" "GREM1" "FRMD3" "CDH4"
## [36] "SERTAD2" "SYCP2" "RP5-864K19.4" "CYP1B1-AS1" "HCG17"
## [41] "C2orf27A"
## [1] "found 28 genes."
## [1] 6
## [1] "CELSR3" "ZNF365" "RBMS3"
## [4] "CLSTN2" "NRG2" "PRICKLE2"
## [7] "ARHGEF3" "RANBP3L" "ADGRV1"
## [10] "FSTL5" "HPSE2" "LRRC3B"
## [13] "POTEG" "CACNA1E" "ZNF521"
## [16] "LINC00970" "XKR9" "AC023469.1"
## [19] "ROR1-AS1" "SATB1-AS1" "LINC01435"
## [22] "RP11-147G16.1" "RP11-154D17.1" "AC013463.2"
## [25] "AC002066.1" "CTC-340A15.2" "USP2-AS1"
## [28] "RP11-696N14.1" "RP1-179N16.6" "LINC01609"
## [31] "RP11-661A12.5" "RMST" "RP11-20D14.3"
## [34] "RP11-396B14.2" "MTRNR2L12" "RMRP_ENSG00000269900"
## [37] "LINC00551" "CH507-513H4.1" "CH507-528H12.1"
## [40] "RP11-596C23.6" "RP4-799O8.1" "RP11-398J12.1"
## [1] "found 17 genes."
## [1] 7
## [1] "SYNDIG1" "PLAT" "FAM149A" "TMEM156"
## [5] "ARMH4" "RP11-493L12.4" "ARHGAP6" "FSTL4"
## [9] "DDX3Y" "PILRA" "TGFB2" "GRK3"
## [13] "ITGB8" "SERPINE1" "BICRAL" "PADI2"
## [17] "OGFRL1" "CDH26" "TIAM2" "SLC2A13"
## [21] "DHRS13" "NCMAP" "GLDN" "CCDC73"
## [25] "NHEJ1" "ZNF846" "CYRIA" "ZDBF2"
## [29] "GCC2-AS1" "AC025171.1" "LNCAROD" "MYO16-AS1"
## [33] "FMN1" "RP11-351A11.1" "RP11-111A21.1" "RP11-707P17.1"
## [37] "RP11-358F13.1" "RP11-404C6.6" "RP11-452F19.4"
## [1] "found 28 genes."
## [1] 8
## [1] "SIGLEC1" "PCSK1N" "MAP3K8" "FLVCR2"
## [5] "F13A1" "ENOSF1" "IFI44L" "CH25H"
## [9] "HERC6" "UBE2Q2" "FHAD1" "TMEM44"
## [13] "ADAMTS19" "ADGRA3" "BEX3" "MT1E"
## [17] "OLR1" "ODF3B" "H2BC4" "MX2"
## [21] "H2BC18" "TMSB4X" "MS4A4E" "RP11-123B3.2"
## [25] "RP5-1101C3.1" "ARHGAP8" "LINC01258" "LINC02196"
## [29] "ZNF10" "RP1-71H24.1" "OVCH1-AS1" "RP11-323I15.5"
## [33] "LINC01572" "RP11-386I14.4" "H2BC8" "H2AC8"
## [37] "RP11-736I24.5" "PLXNC1"
## [1] "found 28 genes."
## [1] 9
## [1] "CALCR" "ZNF532"
## [3] "MBNL3" "OPHN1"
## [5] "MS4A4A" "ADGRG6"
## [7] "LDAH" "MTERF1"
## [9] "PIGC" "LRIG1"
## [11] "PSTPIP2" "PID1"
## [13] "RAB28" "PUS10"
## [15] "TMEM144" "DNAJC24"
## [17] "WDR25" "SDHAF3"
## [19] "PRDX6-AS1" "MAMDC2-AS1"
## [21] "ZNF433-AS1" "LINC00630"
## [23] "RPL34-DT" "LINC01278"
## [25] "RP11-195C7.1" "LINC02432"
## [27] "PVT1" "RP11-130F10.1"
## [29] "LIX1-AS1" "LINC01605_ENSG00000253161"
## [31] "LINC01146" "DISC1FP1"
## [33] "EIF1B-AS1" "RP11-323F24.5"
## [35] "RP4-545L17.11" "PARP8"
## [37] "IL15" "TMEM65"
## [39] "APLF" "KCNE1"
## [41] "ZNF407"
## [1] "found 24 genes."
## [1] 10
## [1] "TPD52" "RPL3" "RPL18A" "RPL19" "RPL34"
## [6] "RPL24" "ATP5F1E" "FGF13" "RPS24" "PRDM5"
## [11] "RPS2" "RPS11" "RPL11" "SPAG16" "RPL32"
## [16] "FAU" "BEND6" "ATG10" "RPL26" "ELAVL4"
## [21] "MRPL1" "RPL38" "RPLP2" "RPS23" "SPATS2L"
## [26] "CPNE4" "RPL12" "RPL23A" "RPL39" "AIF1"
## [31] "DOK6" "SPOCK2" "SLC1A2" "ZMAT4" "LPL"
## [36] "ADARB1" "LILRB3" "SLC5A4-AS1"
## [1] "found 37 genes."
## [1] 11
## [1] "DERA" "SNX24" "ITGA6" "POLA1" "MID1" "SUSD1"
## [7] "APBA1" "MAP2K6" "WLS" "AKAP7" "SLC10A7" "DTD1"
## [13] "METTL25" "LANCL2" "DPH6" "NPL" "IRF8" "MMS22L"
## [19] "NUBPL" "SAMSN1" "BACH1" "C1QC" "TNFRSF13C" "FILIP1L"
## [25] "SLC35G2" "C1QA" "PTPN2" "RTTN" "PROS1" "CCDC7"
## [31] "HGF" "FDFT1" "HACE1" "KLHL24" "COL5A1" "FNBP1L"
## [37] "GOLIM4"
## [1] "found 37 genes."
## [1] 12
## [1] "NEXMIF" "NAV3" "CASS4" "PLCL1"
## [5] "GARNL3" "GIPC2" "UNC80" "TSPAN7"
## [9] "CACNA1D" "RNF180" "CCDC171" "NAV2"
## [13] "ZNF608" "MACROD2" "KCNIP1" "ERC2"
## [17] "COL25A1" "ALOX12-AS1" "LINC00539" "RP11-535M15.1"
## [21] "STX18-AS1" "LINC02232" "MRPS30-DT" "RP4-809F18.1"
## [25] "RP11-370I10.6" "RP11-622O11.6" "COPG2IT1" "RP11-640F22.1"
## [29] "RP11-320L2.1" "DOCK3" "CUX2" "WDR45B"
## [33] "KCND3" "DPP10" "ANKS1B" "KCNIP4"
## [37] "AIDA" "RYR2" "SNHG14"
## [1] "found 26 genes."
## [1] 13
## [1] "MCF2L2" "CYFIP2" "CST3" "STS" "ABCC4" "DOCK10"
## [7] "BCAS3" "FOXO1" "BTG2" "ANO10" "ARHGAP25" "B2M"
## [13] "BTD" "SERPINB9" "XKR6" "DYNC2H1" "RPL41" "RORA"
## [19] "SLC1A3" "DOCK9" "PRKAG2" "RAPGEF1" "PTPRE" "SSH2"
## [25] "SDK1" "MGAT5" "FMNL2" "RUNX1" "CLASP2" "OXR1"
## [31] "LDLRAD4" "GPHN" "CEBPB" "CHD2" "BAIAP2" "MYO1D"
## [37] "PCDH9" "GDI1" "NEAT1"
## [1] "found 38 genes."
## [1] 14
## [1] "TNFRSF21" "JARID2" "ARAP2" "CPSF1" "GRAMD4" "PPP1R15A"
## [7] "CEP170B" "TBL1X" "INTS6" "HSF4" "UBE2R2" "DNAJC12"
## [13] "DCUN1D4" "BBX" "CYTIP" "TSHZ3" "MGAT1" "PHF21A"
## [19] "IQGAP2" "GFOD1" "GNA12" "THRB" "RPP38" "CAMK4"
## [25] "RASSF3" "ASAP1" "RASA2" "CDC42SE2" "SLMAP" "STXBP5"
## [31] "PCDH7" "SH3PXD2B" "CMSS1" "ARL4C" "RALGAPA2" "IARS1"
## [37] "ZNF277" "EFCAB2" "ZSCAN31"
## [1] "found 39 genes."
## [1] 15
## [1] "LRRC74A" "MEIS1" "ZNF707" "HECW1" "PKD1"
## [6] "NCDN" "PTPRN" "ITPKC" "PCSK5" "FLT1"
## [11] "EPHA4" "KDM5B" "NR4A3" "ZC4H2" "AFDN"
## [16] "EMILIN2" "RAMP1" "MACROD1" "MICAL2" "KCNK1"
## [21] "CRIM1" "NPAS3" "CACNA2D1" "PTPRN2" "SORCS3"
## [26] "PALM2AKAP2" "FGF17" "SPTBN4" "UNC5C" "TSHZ2"
## [31] "NELL2" "ZBTB7C" "PBX1" "MIB2" "SLC48A1"
## [36] "MTRNR2L1" "GRIN2B"
## [1] "found 37 genes."
## [1] 16
## [1] "PRKCQ" "FOXP2" "ATF5" "XIST" "GCLC"
## [6] "GCLM" "PRKCH" "WWC3" "ZFAT" "MYO9A"
## [11] "ARHGAP15" "ANKRD12" "ADAP1" "MEGF9" "FOXP1"
## [16] "SEM1" "KIAA0513" "CAMKMT" "FER" "RASGRP3"
## [21] "MERTK" "JAZF1" "ADK" "ST3GAL2" "EPB41"
## [26] "FBXO27" "NEK10" "MTSS1" "MALT1" "FUT10"
## [31] "RESF1" "SLC35E3" "SAMD12" "CSMD1" "MAML2"
## [36] "NPIPB15" "CARD11" "SOGA3" "AC092835.2"
## [1] "found 37 genes."
## [1] 17
## [1] "ADGRD1" "PDE10A" "NEURL2" "BANK1"
## [5] "ADAMTS3" "UCN" "PGBD5" "TMEM151B"
## [9] "HDAC4-AS1" "RP11-445F6.2" "SMCR5" "LINC01515"
## [13] "LINC01277" "RP3-525N10.2" "LINC00271" "LINC02884"
## [17] "AC007682.1" "RP11-142A5.1" "AC073115.6" "BDNF-AS"
## [21] "LINC02211" "RP11-115J16.1" "C5orf17" "RP11-673E1.1"
## [25] "LINC02055" "FAM66D" "MIR100HG" "PRANCR"
## [29] "CTD-2336H13.2" "LINC02073" "CCDC28A-AS1" "RP11-413N10.3"
## [33] "CERNA2" "RP11-221G19.1" "LINC02885" "RP11-237N2.1"
## [37] "RP11-38B6.1" "RP13-52K8.2"
## [1] "found 8 genes."
## [1] 18
## [1] "OSBPL5" "SNCAIP"
## [3] "MGLL" "RPH3A"
## [5] "GDAP1" "CD69"
## [7] "PDE4D" "ZRANB3"
## [9] "CHN1" "CALY"
## [11] "EFCAB11" "RNF157"
## [13] "NRGN" "ABCA5"
## [15] "CPLX1" "KCNMB2"
## [17] "ALG1L9P_ENSG00000248671" "CEROX1"
## [19] "ADAM22" "VCAN"
## [21] "PDE4A" "KCNAB2"
## [23] "RAB27A" "ZNF586"
## [25] "NCS1" "SASH1"
## [27] "HPCAL1" "SH3BP5"
## [29] "SNAP25" "PAM"
## [31] "MSI2" "STARD9"
## [33] "KALRN" "MSRA"
## [35] "CADM1" "PDE4B"
## [37] "KAZN" "UNC13B"
## [39] "MICAL3"
## [1] "found 37 genes."
## [1] 19
## [1] "ETV1" "SCMH1" "IGF1" "PER3" "APBB1IP" "IL1A"
## [7] "IL1B" "IL6ST" "SLC22A23" "TRPC1" "MLIP" "COPG2"
## [13] "NLRP3" "KIF26B" "SFMBT1" "TMEM52B" "DTWD2" "DENND5B"
## [19] "DLEU1" "SLC8A1" "PRKN" "SFMBT2" "MBD5" "LTC4S"
## [25] "LIPE-AS1" "MIR99AHG" "MATK" "RNASET2" "RBFOX1" "PDGFB"
## [31] "LIFR" "HPCAL4" "SLC6A8" "SLC2A5" "FAT3" "RBFOX3"
## [37] "TNFRSF10C" "PCGF5"
## [1] "found 35 genes."
## [1] 20
## [1] "ZFP64" "EFR3B" "EPDR1" "TXNDC16"
## [5] "PARD3B" "GALNT12" "IFT43" "SIRPD"
## [9] "FBN2" "TEX9" "LINC00467" "DISP1"
## [13] "CLIC2" "MAP3K7CL" "AIM2" "ATF7IP2"
## [17] "TMC7" "SPTLC3" "RAB39A" "FSIP2"
## [21] "LEKR1" "LINC01356" "AC097721.2" "RP5-1198O20.4"
## [25] "FSIP2-AS1" "RP11-634B7.4" "CDKN2B-AS1" "LINC00968"
## [29] "STARD4-AS1" "RP11-120A1.1" "RP11-10H3.1" "MIR3142HG"
## [33] "RHOXF1-AS1" "LINC02666" "RP1-111C20.3" "GALNT18"
## [37] "ARHGEF25" "CPEB2-DT" "CTB-41I6.2"
## [1] "found 22 genes."
## [1] 21
## [1] "ERCC8" "OXCT1" "ALDOC" "CCDC18" "DSTN" "PIGK" "IER2"
## [8] "BACE2" "ABAT" "CDK14" "CDK17" "TGFBR3" "PGM1" "NPDC1"
## [15] "TPI1" "SOD2" "PAPOLG" "HSPH1" "CAMK1" "DNAJB2" "UACA"
## [22] "CPNE8" "MSN" "MCPH1" "CFDP1" "PTMS" "PCNT" "GLRX"
## [29] "AGFG1" "FAM20C" "ZDHHC20" "LIMK2" "COL27A1" "HSPA1B" "PPME1"
## [1] "found 35 genes."
## [1] 22
## [1] "ACKR4" "HIVEP2" "MAMLD1" "HDHD5"
## [5] "MAP3K20" "GADD45B" "IL4I1" "LILRB5"
## [9] "HS3ST2" "TREM1" "GPNMB" "NIBAN2"
## [13] "RASGEF1B" "TAMALIN" "IER5" "ATOH8"
## [17] "VMO1" "ADSS1" "ANKRD37" "ZNF395"
## [21] "TPRG1" "H2BU1" "AF064858.6" "AS3MT"
## [25] "FAM229A" "LIMD1-AS1" "DIRC3" "DARS1-AS1"
## [29] "RP11-47I22.3" "AC009505.4" "MIR155HG" "AF064858.8"
## [33] "SELENOP" "LINC02698" "CLEC5A" "SAP30-DT"
## [37] "MYOCOS" "RP11-475M20.2" "CTD-2285E13.1" "RENO1"
## [41] "RP11-134L10.2"
## [1] "found 26 genes."
## [1] 23
## [1] "RIPOR2" "LILRB2" "MCTP2" "ABCA8"
## [5] "MTHFD2L" "RAB37" "ARSJ" "CARNMT1-AS1"
## [9] "PCDH9-AS2" "AC073115.7" "TRG-AS1" "RP11-341N18.1"
## [13] "RP11-120L14.1" "GALNT16" "CDH20" "MYOM1"
## [17] "KATNAL1" "STN1" "ARFGEF3" "ADAM23"
## [21] "MXI1" "ATP8A1" "PCSK2" "PATJ"
## [25] "BTBD11" "PITPNC1" "FBXO32" "ZFYVE28"
## [29] "JAML" "PLPP3" "SNED1" "AMER2"
## [33] "KLF13" "TBC1D10C" "JAKMIP2" "ZHX2"
## [37] "TMTC2" "SSTR2" "CD247" "CCDC71L"
## [41] "LINC01138"
## [1] "found 33 genes."
## [1] 24
## [1] "RASGRP2" "FAM50A"
## [3] "ADGRL1" "SLC26A3"
## [5] "AK1" "DRAM1"
## [7] "CCNG2" "PGGHG"
## [9] "PXDNL" "LRRC4C"
## [11] "CLEC1A" "AMN1"
## [13] "CFAP161" "TNFRSF11B"
## [15] "SEMA3E" "LPCAT4"
## [17] "LINC00910" "LINC00862"
## [19] "LINC02397" "C17orf67"
## [21] "LINC01320" "ARL17B"
## [23] "KLF3-AS1" "SGO1-AS1"
## [25] "AC067959.1" "LINC01762"
## [27] "RP3-467L1.4" "LINC02646"
## [29] "RP11-305L7.3" "RP11-657O9.1"
## [31] "LINC01322" "RP11-17A1.3"
## [33] "RP11-79E3.2" "RP11-81K2.1"
## [35] "SCARNA2_ENSG00000270066" "RP11-154H23.4"
## [37] "RP11-114N19.3" "RP11-344F5.1"
## [39] "AC003099.2"
## [1] "found 18 genes."
## [1] 25
## [1] "MPP2" "IRAK1BP1" "SKA2" "CNTN1" "LRRC7" "CTNNA2"
## [7] "ZFY" "ARHGAP10" "RAPGEF4" "CELF4" "KCNT1" "CPE"
## [13] "MOB3B" "OLFM1" "PDZD2" "KCNH1" "CDH18" "CNKSR2"
## [19] "ME3" "SCN3A" "FMN2" "SYN2" "EDIL3" "NLGN1"
## [25] "CTNND2" "DLGAP1" "C11orf80" "CNTNAP2" "PPM1E" "RIMS2"
## [31] "NRXN1" "OPCML" "RALYL" "OSBP2" "PRKG1" "SYN3"
## [37] "MYT1L" "MAGI2" "GRM7"
## [1] "found 39 genes."
## [1] 26
## [1] "ADAM28" "PROCR" "NEK11" "CCDC170" "SMAD6" "MED12L" "SAMD4A"
## [8] "NSMAF" "LIMCH1" "PHLPP1" "IRAK3" "FKBP5" "USP9Y" "FOXO3"
## [15] "ELL2" "RUNX2" "DOCK6" "ZNF331" "IRAK2" "CCNH" "NHSL1"
## [22] "FAM117B" "FAM13A" "PELI2" "MAP3K6" "USP53" "NEK7" "PDE3B"
## [29] "OTUD1" "LRP1B" "PPIP5K1" "BNC2" "H2AC6" "GPRIN3" "SULF2"
## [36] "PELI1" "CEBPD"
## [1] "found 37 genes."
## [1] 27
## [1] "IPCEF1" "PEX7" "ITPR2" "C3" "STAMBPL1"
## [6] "GSTCD" "FRMD6" "ITGA9" "TBC1D32" "FRMD4A"
## [11] "LRRC8C" "ZMAT3" "ATAD5" "CA8" "SLC9A9"
## [16] "CACNB4" "MEI4" "SCIN" "CLEC16A" "LCP2"
## [21] "PAG1" "CTTNBP2" "RFX3" "RFX2" "RASSF8"
## [26] "ARHGAP22" "PRAM1" "WNT2B" "GYPC" "CSGALNACT1"
## [31] "DIXDC1" "SH3RF1" "DHRSX" "PACS1" "FADS3"
## [1] "found 35 genes."
## [1] 28
## [1] "PKD2L2" "IL7" "SGCE" "MIR4435-2HG"
## [5] "GLIPR1L1" "TTTY14" "MCMDC2" "EYS"
## [9] "RP1-225E12.2" "RP5-1132H15.1" "LANCL1-AS1" "ITGA9-AS1"
## [13] "RMDN2-AS1" "LRIG2-DT" "RP11-775D22.3" "RP11-544A12.8"
## [17] "RP11-506H20.1" "RP11-1H15.2" "RP11-867G2.8" "RP11-571M6.7"
## [21] "RP11-160E2.6" "RP11-703M24.5" "CEACAM16-AS1" "KCNQ1OT1"
## [25] "RP11-74J13.8" "RP11-305E17.8" "RP11-793H13.14" "RP1-18C9.3"
## [29] "RP11-65F13.4" "RP11-13J12.3" "RP11-6G22.1" "RP11-685G9.5"
## [33] "RP11-555K12.4" "RP11-617F9.2" "ST3GAL1" "SLC9A7"
## [37] "PCDH11Y" "APBB3" "H1-10" "RP11-37N22.1"
## [41] "RP11-384C4.7" "RP11-322M13.1"
## [1] "found 11 genes."
## [1] 29
## [1] "PLPP1" "ACER3" "SP140" "CARMIL1"
## [5] "ZNF821" "RCAN3" "PLAGL1" "SSPN"
## [9] "PUDP" "SPATA6" "TBC1D14" "EPHB2"
## [13] "ARHGAP20" "SLC49A4" "NKD1" "WDPCP"
## [17] "C11orf49" "CD226" "DENND2B" "FGGY"
## [21] "B3GNT5" "PCED1B" "SCFD2" "FIRRE"
## [25] "LINC02649" "FTCDNL1" "RP11-162D16.2" "RP11-202G18.1"
## [29] "RFX3-AS1" "RP11-557H15.4" "LINC00884" "LINC01184"
## [33] "LINC02762" "LINC02328" "RP11-154H12.3" "TSIX"
## [37] "RP11-323P17.2" "MIR223HG" "RP11-419I17.1" "SEC14L1"
## [1] "found 24 genes."
## [1] 30
## [1] "HTR2B" "TAGAP" "PNMA3" "TWIST2" "NFIX"
## [6] "TNS1" "RNF24" "RNMT" "BNIP3L" "GYS1"
## [11] "ARRDC2" "GBE1" "RLF" "SPP1" "IQSEC2"
## [16] "SOX5" "IQSEC1" "SLC25A37" "RIT2" "AGPAT5"
## [21] "MAPK13" "SSBP3" "ETS2" "ABCG1" "ABCA1"
## [26] "DDIT4" "SNTB2" "CRADD" "PPP1R3B" "BNIP3"
## [31] "FAM210A" "CHST15" "H1-0" "RGL3" "AC093818.1"
## [36] "RP11-13N12.1" "FMNL1-DT"
## [1] "found 34 genes."
## [1] 31
## [1] "PDK4" "NLRP1" "CPED1" "PEBP4"
## [5] "GPAT3" "CFAP74" "GASK1A" "TENM4"
## [9] "SETBP1" "C4orf19" "DEPTOR" "MIR31HG"
## [13] "CYSLTR1" "KCNQ3" "RTN4RL1" "CLEC9A"
## [17] "LINC01285" "RP11-131L23.1" "LINC01357" "AC105760.2"
## [21] "KIF9-AS1" "HDAC2-AS2" "HMGA1P4" "MIR4300HG"
## [25] "CTB-161M19.4" "ZFPM2-AS1" "LINC01301" "RP11-946L16.1"
## [29] "RP11-187O7.3" "MRC1" "ATP6V0D1-DT" "RP11-495L19.1"
## [33] "RP11-437L7.2" "RP11-168F24.3" "RP11-4F5.3" "KCNQ2"
## [37] "HTR1E" "KCNQ5" "RP11-249L21.6"
## [1] "found 19 genes."
## [1] 32
## [1] "TTC7A" "NIPAL2"
## [3] "GAREM1" "SESN3"
## [5] "PLXDC1" "HESX1"
## [7] "NMNAT3" "LIPC"
## [9] "PLD4" "CX3CR1"
## [11] "ACYP2" "ZDHHC14"
## [13] "CATSPERE" "SPATA13_ENSG00000182957"
## [15] "RNLS" "B3GLCT"
## [17] "AC003090.1" "ENTPD3-AS1"
## [19] "TMEM72-AS1" "CTA-292E10.6"
## [21] "TEX41" "LMCD1-AS1"
## [23] "RP13-188A5.1" "MIR646HG"
## [25] "HCG22" "ZRANB2-AS2"
## [27] "LINC01376" "RNF217-AS1"
## [29] "MEF2C-AS1" "RP11-319G6.1"
## [31] "RP11-381K20.2" "RP11-692D12.1"
## [33] "GMDS-DT" "RP11-679C8.2"
## [35] "C8orf37-AS1" "RP11-541P9.3"
## [37] "RP11-511B23.2" "LINC00907"
## [39] "MIR222HG" "RP11-111G13.1"
## [41] "RP11-685G11.1"
## [1] "found 15 genes."
## [1] 33
## [1] "MUSK" "ANGPT2" "ECM2" "FMO5" "BCL2A1"
## [6] "ZDHHC19" "BEAN1" "GLYATL1" "MOBP" "RP11-621L6.2"
## [11] "SLC2A3" "ABCA7" "PLEKHH3" "ANO8" "RAP1GAP"
## [16] "HIF3A" "CHI3L1" "BTG1" "CEMIP2" "HILPDA"
## [21] "ADCY3" "RGS16" "TMEM140" "ST18" "PLIN2"
## [26] "LYPD5" "CCDC107" "ANKZF1" "NFIL3" "ALDH1A1"
## [31] "ADCY5" "RBM44" "CD55" "ERO1A" "SH3BGRL2"
## [36] "STARD10" "SLC12A8" "HIF1A-AS3"
## [1] "found 36 genes."
## [1] 34
## [1] "ATP8B1" "SLC5A9" "SHOC1" "ENO4"
## [5] "INSYN2B" "ANKUB1" "AC002463.3" "ELMO1-AS1"
## [9] "TMLHE-AS1" "AC096558.1" "RP4-568F9.6" "AC083884.8"
## [13] "AC037445.1" "CPB2-AS1" "MYCBP2-AS1" "DIAPH2-AS1"
## [17] "CCDC200" "AC018890.6" "LINC01877" "MEF2C-AS2"
## [21] "CTD-2015H6.3" "RHOQ-AS1" "RP11-268P4.5" "AP000487.6"
## [25] "RP11-638I2.8" "LINC02316" "USP3-AS1" "RP11-815J21.4"
## [29] "RP11-16B9.1" "PRKCA-AS1" "RP11-16C1.3" "RP11-793A3.2"
## [33] "RP11-58G13.1" "RP1-256G22.2" "CTD-2282P23.2" "DISC2"
## [37] "RP11-314L11.1" "RP11-261A24.1" "RP11-1H15.4" "RP11-1146N6.3"
## [41] "SLC26A7"
## [1] "found 8 genes."
## [1] 35
## [1] "HHAT" "XAF1" "FBXL13" "PAQR3" "LINC00624"
## [6] "MSR1" "PDE8A" "RGS1" "DARS1" "GTDC1"
## [11] "SRGN" "RGL1" "MYO10" "TNFAIP8" "ARHGAP18"
## [16] "RSU1" "HTR7" "ARID5B" "NGLY1" "ACSL1"
## [21] "FRRS1" "ACOT11" "CDCP1" "RHOBTB3" "MARCHF8"
## [26] "ALCAM" "KLHL6" "MFSD4B" "TNFAIP8L3" "MITF"
## [31] "DPYD" "PARVB" "CTD-3088G3.8" "UBXN2B" "PIK3IP1-DT"
## [36] "MIR181A1HG" "CTD-2643I7.5" "IFITM10" "SBF2-AS1"
## [1] "found 33 genes."
## [1] 36
## [1] "CRYM" "IGSF11" "GLT1D1" "TSBP1-AS1"
## [5] "KIF5C-AS1" "MEIKIN" "MTRNR2L8" "PSMD7-DT"
## [9] "SYT7" "COL5A3" "IGSF9B" "NALCN"
## [13] "DNAH6" "CHD5" "CSMD2" "CBLN2"
## [17] "CFAP251" "PDZRN4" "STXBP6" "CXXC5"
## [21] "CADM2" "SRRM3" "ADGRB1" "NRG3"
## [25] "SLIT1" "CR1L" "RORB" "FAM153CP"
## [29] "BASP1-AS1" "MIAT" "TRHDE-AS1" "RP11-259O2.1"
## [33] "LINC01414" "CTC-535M15.2" "RP11-429A20.3" "RP11-368L12.1"
## [37] "LINC00558" "U91319.1" "RP11-436D23.1" "RP5-1015P16.1"
## [41] "RP11-335E8.3"
## [1] "found 24 genes."
## [1] 37
## [1] "ICA1" "PRDM11" "ST6GAL1" "SLC26A4"
## [5] "PODXL2" "AOPEP" "LY96" "SMIM14"
## [9] "PRMT9" "GPR34" "GAP43" "CAPS2"
## [13] "CDIN1" "SRGAP3" "CHSY3" "C12orf75"
## [17] "LINC00894" "LINC01684" "RP11-37B2.1" "RP11-630C16.2"
## [21] "RP11-574F11.4" "STAB1" "SESN1" "TMED8"
## [25] "IL27RA" "NCOA7" "FRMD4B" "TMEM115"
## [29] "CHSY1" "SLC41A2" "TLR2" "DHRS3"
## [33] "ROBO1" "RNF150" "LONRF3" "TRNAU1AP"
## [37] "TLR5" "ZC3H6"
## [1] "found 33 genes."
## [1] 38
## [1] "CECR2" "NME3" "ABCC1" "OGN" "PLGRKT"
## [6] "IFIT3" "IFIT2" "CENPK" "SAT1" "RTN4IP1"
## [11] "PCBD2" "ITM2C" "ERMN" "TET1" "LPAR6"
## [16] "PTH2R" "ADGRG5" "FAM227B" "RIC3" "TLN2"
## [21] "NAALADL2" "ZFP36L1" "IFIT1" "DNAH14" "ZNRF1"
## [26] "CH17-55D9.1" "RP6-91H8.6" "RP4-681L3.3" "ATP9A" "RGCC"
## [31] "TGFBI" "ATP8B2" "KIF5C" "KLC2" "MAMDC4"
## [36] "IFNLR1" "GK"
## [1] "found 34 genes."
## [1] 39
## [1] "PLEK" "CYREN" "RAB38" "MMP24"
## [5] "OMD" "TMEM241" "IER3" "AGBL3"
## [9] "NLGN4Y" "CYTL1" "IRAG1-AS1" "H2AC20"
## [13] "AC023590.1" "ARHGAP26-AS1" "ZNF451-AS1" "AC105461.1"
## [17] "ALG13-AS1" "ARHGAP15-AS1" "IPO9-AS1" "RAP2C-AS1"
## [21] "UFL1-AS1" "RP11-528G1.2" "FBXO30-DT" "KDM4A-AS1"
## [25] "BCL2L1-AS1" "RP11-544A12.4" "DENND6A-AS1" "ZBTB20-AS5"
## [29] "GPRC5D-AS1" "RP11-434H14.1" "LINC00639" "RP11-106M3.3"
## [33] "RNF213-AS1" "H2BC7" "RP11-121C2.3" "RP11-19D22.1"
## [37] "RP11-622I12.1" "RP11-458A7.1" "RP11-21M24.6" "RP11-314E10.1"
## [41] "RP11-399K19.1"
## [1] "found 12 genes."
## [1] 40
## [1] "ANGPTL1" "C11orf65" "COL5A2" "SPDYE2"
## [5] "MTCP1" "RP11-321C24.1" "DOCK4-AS1" "RP11-165F24.3"
## [9] "AC017101.10" "RP11-526K17.2" "RP11-575L7.8" "RP1-117O3.2"
## [13] "KCNMA1-AS1" "LINC00960" "RP11-712B9.2" "ANK2-AS1"
## [17] "CTD-2227I18.1" "LINC02742" "RP11-39E3.3" "CTD-3239E11.2"
## [21] "RP11-624C23.1" "RP11-463D19.1" "CTD-2537O9.1" "RP11-493L12.3"
## [25] "RP11-713N11.4" "CTD-2647E9.3" "RP11-317G6.1" "RP11-516C1.1"
## [29] "LMO7-AS1" "RP11-66H6.3" "LINC00621" "RP11-737O24.2"
## [33] "TCF4-AS1" "RP11-53B2.3" "RP11-126O1.4" "CTD-3149D2.4"
## [37] "RP4-769N13.7" "H2AC19" "RP11-275G7.2" "GS1-98E2.1"
## [41] "RP1-80B9.4" "CTD-2021K4.2"
## [1] "found 6 genes."
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 4171674 222.8 10243768 547.1 NA 10243768 547.1
## Vcells 8967049 68.5 29538339 225.4 65536 29538339 225.4
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] stringr_1.5.0 limma_3.54.2 tidyr_1.3.0 ggpubr_0.6.0
## [5] ggplot2_3.4.2 data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.10 png_0.1-8 Biostrings_2.66.0
## [4] digest_0.6.31 utf8_1.2.3 R6_2.5.1
## [7] GenomeInfoDb_1.34.9 backports_1.4.1 stats4_4.2.3
## [10] RSQLite_2.3.1 evaluate_0.20 httr_1.4.6
## [13] pillar_1.9.0 zlibbioc_1.44.0 rlang_1.1.0
## [16] rstudioapi_0.14 car_3.1-2 jquerylib_0.1.4
## [19] blob_1.2.4 R.oo_1.25.0 R.utils_2.12.2
## [22] S4Vectors_0.36.2 rmarkdown_2.21 labeling_0.4.2
## [25] RCurl_1.98-1.12 bit_4.0.5 munsell_0.5.0
## [28] broom_1.0.4 compiler_4.2.3 xfun_0.39
## [31] pkgconfig_2.0.3 BiocGenerics_0.44.0 htmltools_0.5.5
## [34] tidyselect_1.2.0 KEGGREST_1.38.0 GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1 IRanges_2.32.0 fansi_1.0.4
## [40] crayon_1.5.2 dplyr_1.1.2 withr_2.5.0
## [43] R.methodsS3_1.8.2 bitops_1.0-7 grid_4.2.3
## [46] jsonlite_1.8.4 gtable_0.3.3 lifecycle_1.0.3
## [49] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
## [52] cli_3.6.1 stringi_1.7.12 cachem_1.0.7
## [55] carData_3.0-5 farver_2.1.1 XVector_0.38.0
## [58] ggsignif_0.6.4 bslib_0.4.2 generics_0.1.3
## [61] vctrs_0.6.2 RColorBrewer_1.1-3 org.Hs.eg.db_3.16.0
## [64] tools_4.2.3 bit64_4.0.5 Biobase_2.58.0
## [67] glue_1.6.2 purrr_1.0.1 abind_1.4-5
## [70] fastmap_1.1.1 yaml_2.3.7 AnnotationDbi_1.60.2
## [73] colorspace_2.1-0 rstatix_0.7.2 memoise_2.0.1
## [76] knitr_1.44 sass_0.4.5